Frank Schacherer Homepage
home technology bibliography


Jay Yellen and Jonathan L. Gross Graph Theory & Its Applications *** 0849339820
What's nice about this book is that they give you all the term definitions, and a lot of drawings to boot, so you can visually understand what they are talking about. This makes it usually very easy to grasp the point. Much more so, in my opinion at least, than reading page after page of math formulas. There's also the algorithms, even though you can get most of those from an aglorithm book, if you already have one.
J. D. Murray and S. A. Levin (Editor) Mathematical Biology (Biomathematics, Vol 19) *** 038757204X
Eberhard O. Voit Computational Analysis of Biochemical Systems *** 0521785790
A great intro to simulation, differenetial eqation models of biochemical networks.
Neill Gershernfeldt The Nature of mathematical modeling *** 0521570956
This one is way over my head math-wise. So take this review with a grain of salt. A lot of topics are covered, but I think not in a way that is detailed enough to learn about them. It might be enough to remind you how things generally work, when you already know them, like some notes made for yourself. Also, for my purposes, only the last third is interesting, when it comes to generating models from data. The first two thirds deal with analytical models, mostly based on differential equations of all kinds, where you can write down the full model, paramethers and all and just have to solve it, and with their numerical solution in case that is not possible.
John H. Holland Hidden Order - How Adaption builds Complexity *** 0201442302
A very observant little book that summarizes properties of complex adaptive systems, than goes on how to build a minimal yet expressive simulation of such systems. The general part is better. Holland also invented Classifier Systems, if I'm informed correctly.
Dieter Jungnickel Graphen, Netzwerke und Algorithmen **  
M. Mitchell Waldrop Complexity ** 0671872346
Wolfgang Reisig Petrinetze: eine Einführung ** 354016622X
It's a bit dated and does not cover later developments like colored nets well, and it's dry as dust to read. A reference on definitions but not a good introduction to the field.
Stuart A. Kaufmann The Origins of Order: Self Organisation and Selection in Evolution ** 0195079515

Journal articles

Daniel T. Gillespie A General Method For Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions 1976 J. Chem. Physics 22, 403-434
Daniel T. Gillespie Exact stochastic simulation of coupled chemical reactions 1977 J. Phys. Chem. 81(25), 2340-2361
M. Kohn and W. Letzkus A Graph-theoretical Analysis of Metablolic Regulation 1982 J. Theor. Biol. 100, 293-304
D. Bray Intracellular signalling as a parallel distributed process 1990 J. Theor. Biol. 143(2), 215-31
M. C. Kohn and D. R. Lemieux Identification of regulatory properties of metabolic networks by graph theoretical modeling 1991 J. Theor. Biol. 150, 3-25
D. L. Brutlag and A. R. Galper and D. H. Millis Knowledge-based simulation of DNA metabolism: prediction of enzyme action 1991 CABIOS 7(1), 9-19
V. N. Reddy and M. L. Mavrovouniotis and M. N. Liebman Petri Net Representations in Metabolic Pathways 1993 ISMB Proceedings 1993, 328-336
P. D. Karp and S. M. Paley Representations of Metabolic Knowledge: Pathways 1994     
D. Bray and S. Lay Computer Simulated Evolution of a Network of Cell-Signaling Molecules 1994 BJ 66, 972-77
Adam Arkin and John Ross Computational Functions in Biochemical Reaction Networks 1994 Biophys. J. 67, 560-578
Try to show signaling interactions as boolean, but fail, as only 'fuzzy' boolean
H. H. McAdams and L. Shapiro Circuit Simulation of Genetic Networks 1995 Science 269, 650-56
Harlie H. McAdams and Adam Arkin Stochastic mechanisms in gene expression 1997 Proc. Natl. Acad. Sci. USA 94, 814-819
F. J. Brandenburg and M. Jünger and P. Mutzel Algorithmen zum automatischen Zeichnen von Graphen 1997 Informatik Spektrum 27(4), 199-207
Adam Arkin and Peidong Shen and John Ross A Test Case of Correlation Metric Construction of a Reaction Pathway from Measurements 1997 Science 277, 1275-1279
Application of CMC abd MDS (multi-dimensional scaling) on a test case, includes short description of the computational methods, which proved surprisingly robust.
B. N. Kholodenko and J. B. Hoek and H. V. Westerhoff and G. C. Brown Quantification of information transfer via cellular signal transduction pathways 1997 FEBS Letters 414, 430-434
Zhi-Long Xiu and An-Ping Zeng and Wolf-Dieter Deckwer Model analysis concerning the effects of growth rate and intracellular tryptophan level on the stability and dynamics of tryptophan biosysnthesis in bacteria 1997 J. Biotechnology 58, 125-140
William M. Mounts and Michael N. Liebman Application of Petri Nets and Stochastic Activity Nets to Modeling Biological Pathways and Processes 1997 Int. J. Comp. Sim.   
W. M. Mounts and M. N. Liebman Qualitative modeling of normal blood coagulation and its pathological states using stochastic activity networks. 1997 Int. J. Biol. Macromol. 20(4), 265-281
Harley H. McAdams and Adam Arkin Stochastic mechanisms in gene expression 1997 Proc. Natl. Acad. Sci. USA 94, 814-819
Harlie H. McAdams and Adam Arkin Simulation of procaryotic genetic circuits 1998 Annu. Rev. Biophys. Biomol. Struct. 27, 199-224
Chiou-Hwa Yuh and Hamid Bolouri and Eric H. Davidson Genomic Cis-Regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene 1998 Science 279, 1896-1902
Christophe H. Schilling and Bernhard O. Palsson The underlying pathway structure of biochemical reaction networks 1998 Proc. Natl. Acad. Sci. USA 95, 4193-4198
Vgl. Schuster
R. Hofestädt and S. Thelen Quantitative Modeling of Biochemical Networks 1998 In Silico Biol. 1, 0005
T. Takai-Igarashi and T. Kaminuma A Pathway Finding System for the Cell Signaling Networks Database 1998 In Silico Biol. 1, 0012
Adam Arkin and John Ross and Harley H. McAdams Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage $lambda$-infected textsl Escherichia coli Cells 1998 Genetics 149, 1633-1648
Marasu Tomita and others E-CELL: software environment for whole-cell simulation 1998 Bioinformatics 15, 72-84
A. U. Igamberdiev Foundations of metabolic organization: coherence as a basis of computational properties in metabolic networks 1999 BioSystems 50, 1-16
Michael J. Fisher and Raymond C. Paton and Koichiro Matsuno Intracellular signalling proteins as 'smart' agents in parallel distributed processes 1999 BioSystems 50, 159-171
Robert Küffner and Ralf Zimmer and Thomas Lengauer Pathway Analysis in Metabolic Databases via Differential Metabolic Display 1999 GCB   
R. Somogyi and S. Fuhrmann Distributivity, a general information theoretic network measure, or why the whole is more than the sum of ist parts 1999 Proceedings of the International Workshop on Information Processing in Cells and Tissues   
D. Thieffry and D. Romero The modularity of biological regulatory networks 1999 BioSystems 50, 49-59
E. Selkov and others Mathematical simulation and analysis of cellular metabolism and regulation 1999 Bioinformatics 15(9), 749-758
S. Schuster and T. Dandekar and A. D. Fell Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering 1999 TIBTECH 17, 53-60
I. M. De la Fuente Diversity of temporal self-organized behaviours in a biochemical system 1999 BioSystems 50, 83-97
J. Schaff and L. M. Loew The virtual cell 1999 PSB   
R. S. Erb and G. S. Michaels Sensitivity of Biological Models to Errors in Parameter Estimates 1999 PSB   
E. M. Marcotte and M. Pellegrini and M. J. Thompson and T. O. Yeates and D. Eisenberg A combined algorithm for genome-wide prediction of protein function. 1999 Nature 402, 83-6
Sui Huang Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery 1999 J. Mol. Med. 77, 469-480
5000ft overview
T. Pfeiffer and I. S'anchez-Valdenebro and J. C. Nuno and F. Montero and S. Schuster METATOOL: for studying metabolic networks 1999 Bioinformatics 15(3), 251-257
Andrew Wuensche Classifying cellular automata a utomatically: Finding gliders, filtering, and relating space-time patterns, attractor basins, and the Z parameter 1999 Complexity 4(3), 47-66
H. L. Hartwell and J. J. Hopfield and S. Leibler and A. W. Murray From molecular to modular cell biology 1999 Nature 402(SUPP), C47-C52
B. Schönfisch and A. de Roos Synchronous and asysnchronous updating in cellular automata 1999 BioSystems 51, 123-143
G. Wenig and U. S. Bhalla and R. Iyengar Complexity in Biological Signaling Systems 1999 Science 284, 92-96
E. M. Marcotte and M. Pellegrini and H. L. Ng and D. W. Rice and T. O. Yeates and D. Eisenberg Detecting protein function and protein-protein interactions from genome sequences. 1999 Science 285, 751-3
L. Mendoza and D. Thieffry and E. R. Alvarez-Buylla Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis 1999 Bioinformatics 15(07), 593-606
T. R. Golub and D. K. Slonim and P. Tamayo and C. Huard and M. Gaasenbeek and J. P. Mesirov and H. Coller and M. L. Loh and J. R. Downing and M. A. Caligiuri and C. D. Bloomfield and E. S. Lander Molecular classification of cancer: class discovery and class prediction by gene expression monitoring 1999 Science 286, 531-537
seminal paper
Ting Chen and Hongyu L. He and George M. Church Modeling Gene Expression with differential equations 1999 PSB   
interesting math
Vassily Hatzimanikatis and Kevin H. Lee Dynamical Analysis of Gene Networks Requires Both mRNA and Protein Expression Information 1999 Metabolic Engineering 1, 275-281
Cool Ref about feedback cycles
D. C. Weaver and C. T. Workman and G. D. Stromo Modeling regulatory networks with weight matrices 1999 PSB   
P. D'haeseleer and S. Liang and R. Somogyi Gene Expression Data Analysis and Modeling 1999 PSB   
V. Krishnamurthy and E. V. Krishnamurthy Rule-based programming paradigm: a formal basis for biological, chemical and physical computation 1999 BioSystems 49, 205-228
U. S. Bhalla and R. Iyengar Emergent Properties of Networks of Biological Signaling Pathways 1999 Science 283, 381-387
I. Rojdestvenski and M. Cottam and Y.-I. Park and G. Öquist Robustness and time-scale hierarchy in biological systems 1999 BioSystems 50, 71-82
Hartmann Genrich and Robert Küffner and Klaus Voss Executable Petri Net Models for the Analysis of Metabolic Pathways 2000 unpublished   
Solid application of Design/CPN to metabolic networks.
Drew Endy and Lingchong You and Ian J. Molineux Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes 2000 Proc. Natl. Acad. Sci. USA 97, 5375-5380
Peter D. Karp An ontology for biological function based on molecular interactions 2000 Bioinformatics 16, 269-285
Atul J. Butte and Pablo Tamayo and Donna Slonim and Todd R. Golub and Isaac S. Kohane Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks 2000 Proc. Natl. Acad. Sci. USA 97, 12182-12186
Application of the relevance network approach, together with entropy based filetring. Second paper on RelNets.
Takako Takai-Igarashi and Tsuguchika Kaminuma A Pathway Finding System for the Cell Signaling Networks Database 2000 In Silico Biol. 1, 980112
Michael A. Gibson and Jehoshua Bruck Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels 2000 J. Chem. Physics 104, 1876-1889
Daniel T. Gillespie The chemical Langevien equation 2000 J. Chem. Physics 113(1), 297-305
Christopher V. Rao and Adam P. Arkin Control Motifs in Intracellular Regulatory Networks 2000     
Reviews methods in network analysis: MCA, elementary flux modes. For gene regulatory nets boolean, diff. eqs and stochastic simulation.
Ioannis Xenarios and Esteban Fernandez and Lukasz Salwinski and Xiaoqun Joyce Duan and Michael J. Thompson and Edward M. Marcotte and David Eisenberg DIP: The Database of Interacting Proteins: 2001 update 2001 Nucleic Acids Res. 29(1), 239-241
Steven H. Strogatz Exploring complex networks 2001 Nature 410, 268-276
A good review about the amenability of networks/dynamic systems to mathematical analysis. Either they are homogenously structured and thus can be handled statistically, or they have a complex structure, and we only can resort to topology and detailed simulation.
Thomas Pfeiffer and Stefan Schuster and Sebastian Bonhoeffer Cooperation and Competition in the Evolution of ATP-Producing Pathways 2001 Science 292, 504-506
Cool little paper compares ATP production by slow high-yield respiration and fast low-yield fermentation. With Competition (eg. for an external food source) respiration looses to fermentation. With Cooperativity (eg. multicellular organism with internalized food), respiration wins.
H. Jeong and S. P. Mason and A.-L. Barabasi and Z. N. Oltvai Lethality and centrality in protein networks 2001 Nature 411, 41-42
Shows power-law for number of connections in interaction databases, and that knoking out a highly connected node has high probability to fundamentally change the network, while a random knockout will not have much effect.
Drew Endy and Roger Brent Modelling cellular behaviour 2001 Nature 409, 391-395
General discussion of the problem of limited data
Christian von Mering and Roland Krause and Berend Snel and Michael Cornell and Stephen G. Oliver and Stanley Fields and Peer Bork Comparative assessment of large-scale data sets of protein-protein interactions 2002 Nature DOI 10.1038/750, 1-5
Compares Y2H, TAP, HMS-PCI, correlated mRNA, synthetic lethality and in silico genomic comparison (gene clusters, conserved operons, fusion proteins) for finding protein-protein interaction vs. hand-annotated set in yeast. All methods are highly unreliable (> 50 percent error), but combinations are not. Estimate 30.000 interactions in yeast. Good references.
E. Ravasz and A. L. Somera and D. A. Mongru and Z. N. Oltvai and A. L. Barabasi Hierarchical organization of modularity in metabolic networks. 2002 Science 297(5586), 1551-5
Hartmut Scheel and Stefan Tomiuk and Kay Hofmann A common protein interaction domain links two recently identified epilepsy genes 2002 Human Molecular Genetics 11(15), 1757-1762
Sequence-analysis based, nice.
Mor Peleg and Iwei Yeh and Russ B. Altman Modelling biological processes using workflow and Petri Net models 2002 Bioinformatics 18(6) 
Daniel Hanisch and Alexander Zien and Ralf Zimmer and Thomas Lengauer Co-Clustering of Biological Networks and Gene Expression Data 2002 Bioinformatics 18(Suppl 1), 145S-154S
Combinartion of network distance and expession clustering with a squashing function
E. Demir and O. Babur and U. Dogrusoz and A. Gursoy and G. Nisanci and R. Cetin-Atalay and M. Ozturk PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. 2002 Bioinformatics 18(7), 996-1003
Similar my Ph.D. work on Transpath. Nice graphics. Compound graphs and Meta-reactions that contain subnets, too.
Xianghong Zhou and Ming-Chih J. Kao and Wing Hung Wong Transitive functional annotation by shortest-path analysis of gene expression data 2002 Proc. Natl. Acad. Sci. USA 99(20), 12783-12788
Using transitive correlation to build a graph between genes. Then check for shared annotation in shortest paths between nodes in that graph, assigning shared (parental) annotation from GO.
T. Oyama and K. Kitano and K. Satou 2 and T. Ito Extraction of knowledge on protein-protein interaction by association rule discovery 2002 Bioinformatics 18(5) 
Kam D. Dahlquist and Nathan Salomonis and Karen Vranizan and Steven C. Lawlor and Bruce R. Conklin GenMAPP, A New Tool for Viewing and Analyzing Microarray Data on Biological Pathways 2002 Nature Genetics   
Short advertisment for GenMAPP.
Upinder S. Bhalla The chemical organization of signaling interactions 2002 Bioinformatics 18(6) 
Anne-Claude Gavin and Giulio Superti-Furga and others Functional organization of the yeast proteome by systematic analysis of protein complexes 2002 Nature 415, 141-147
Complex identification with TAP and MALDI-TOF MS from 1.700 genes yielding 230 complexes, some found by multiple bait. Interesting are statistical data about complexes; finding of new complex members and assignment of function to orthologues in the matching human complexes; and proteins shared between complexes: using these a complex-network is constructed. (Note to me: one could see binary interactions as a complex with two members, unifying complexes and binteractions.)

PhD Thesis

Carl Jason Morton-Firth Stochastic Simulation Of Cell Signalling Pathways 1998 University of Cambridge
Good intro and overview
Frank Schacherer An object-oriented database for the compilation of signal transduction pathways 2001 Technical University of Braunschweig
Transpath is an information system on signal-transduction networks. It focuses on pathways involved in the regulation of transcription factors. Molecules and reactions are stored in an object-oriented database, together with information about their location, quality, family relationships and signaling motifs. Also stored are links to other databases and references to the original literature. Transpath differentiates between the states of a signal molecule and can describe the reaction mechanisms. It used to be available over the web through a Servlet-based interface. Nowadays it is distributed by Biobase Gmbh ( Pathway query mechanisms and several kinds of display are provided for the database in addition to text-based queries and information on single entries.

Conference presentations, posters and demos

S. Schuster and C. Hilgetag and R. Schuster Determining Elementary Modes orf Functioning in Biochemical Reaction Networks at Steady State 1993 Proceedings of the Second Gauss Symposium  
Intro to the flux mode concept
David Heckerman and Dan Geiger and David Maxwell Chickering Learning Bayesian Networks: The Combination of Knowledge and Statistical Data 1994 KDD Workshop 85-96
Rudolf Kruse and Christian Borgelt Data Mining with Graphical Models 1998 KI - Kunstliche Intelligenz 3-16
Thomas Schlitt and Alvis Brazma Reverse Engineering of Gene Regulatory Networks: a Finite State Linear Model 2000 GCB Conference Proceedings  
A. J. Hartemink and D. K. Gifford and T. S. Jaakkola and R. A. Young Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks 2001 Proceedings of the 6th Pacific Symposium on Biocomputing 422-433
A. Wuensche Genomic Regulation modeled as a network with basins of attraction    
Alexander Spirov and others Deciphering the genetic networks: inferring gene relationships from expression data for Drosophila segmentation genes
R. Somogyi Many to One Mappings as a Basis For Life 1997
R. Somogyi Genetic Network Inference in Computational Models and Applications to Large-Scale Gene Expression Data    

PhD Thesis

Bas Dutilh Analysis of data from microarray expperiments, the state of the art in gene network reconstruction 1999 Utrecht University
Good literature review